The Faslane SSN Berthing Project started in May 2004 and was due for completion in May 2009.
But the job is still not finished following construction problems.
The scheme had already bust its original timetable when the main jetty was damaged during its installation in July 2009 when water leaked into the structure.
The Ministry of Defence confirmed to the Enquirer that the contract was still not finished.
A spokesperson said: “MoD is working with the Prime Contractor to complete the SSN Berthing Facility as quickly as possible.
“The delay in the delivery of the project does not affect the operational capability which is delivered by the existing facilities.”
The scheme was the first prime contract project awarded by Defence Estates for Defence Equipment and Support.
Morgan Sindall became a joint venture partner in the project in 2007 when it bought parts of Amec.
An Amec spokesman said: “We continue to support our customer in bringing this complex project to a satisfactory close and are anticipating completing it later this year.”
Morgan Sindall declined to comment.